ZHENG, Zongli (鄭宗立)

Prof. Zheng received his PhD degree in medical epidemiology from Karolinska Institutet in 2011 and completed a postdoctoral training at Massachusetts General Hospital and Harvard Medical School with support from the Swedish Research Council International Postdoc Fellowship. In July 2015, he joined the Department of Biomedical Sciences at City University of Hong Kong.

Research Interests

Our contribution to precision medicine includes the invention of the AMP technology that has accelerated gene fusion discovery. Following initial clinical implementations in top U.S. hospitals (MSK Solid Fusion, MGH NGS Fusion, etc.), the AMP technology has been adopted globally for robust gene fusion detection to guide targeted therapies for cancer patients. We have also developed the GUIDE-seq method that has become a widely used reference for genome-wide unbiased profiling of CRISPR edits. Currently, we focus on:

• Precision genome editing – to improve CRISPR-based precision genome editing for treating diseases rooted in altered DNA bases or chromosomal structures.
• Liquid biopsy – to identify molecular determinants and circulating signatures for cancer monitoring, diagnosis and, ultimately, prevention.

Current PhD Students

Yufan Bao (B.Sc., Hong Kong PolyU, 2020)
Limei Ai (B.Sc., Minzu Uni. China, 2018; M.Sc., Peking Union Medical College, 2021)
Miao Yu (M.D., Sun Yat-Sen Uni., 2018; M.Sc., Sun Yat-Sen Uni., 2021)
Shifeng Lian (M.D./M.Sc., Sun Yat-Sen Uni., 2018, in KI Lab)
Weiwei Bian (B.Sc./M.Sc., Shandong Uni., 2018, in KI Lab)
Zihua Jiang (B.Sc., Sun Yat-Sen Uni., 2019, in KI Lab)

Selected Recent Publications

(For full list: Google Scholar)

Selected recent publications

1. Lian S, Lu C, Li F, Yu X, Ai L, Wu BH, Gong X, Zhou W, Liang X, Zhan J, Yuan Y, Fang F, Liu Z^#, Ji M^#, Zheng Z^#. Monitoring hepatocellular carcinoma using tumor content in circulating cell-free DNA. Clinical Cancer Research (2024).
2. Song Z*, Lian S*, Mak S*, Chow ZY*, Xu C, Wang W, Keung HY, Lu C, Kebede TF, Gao Y, Cheuk W, Cho CS, Yang M, Zheng Z. Deep RNA sequencing revealed fusion junctional heterogeneity may predict crizotinib treatment efficacy in ALK-rearranged non-small cell lung cancer. Journal of Thoracic Oncology (2022) 17:264-276
3. Song Z, Lu C, Xu C, Zheng Z. Noncanonical gene fusions detected at the DNA level necessitate orthogonal diagnosis methods before targeted therapy. Journal of Thoracic Oncology (2021) 16:344-348
4. Choi GCG, Zhou P, Yuen CTL, Chan BKC, Xu F, Bao S, Chu HY, Thean D, Tan K, Wong KH, Zheng Z, Wong ASL. Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nature Methods (2019) 16:722-730.
5. Tan Y*, Chu HY*, Bao S, Hoang DA, Kebede TF, Xiong W, Ji M, Shi J^#, Zheng Z^#. Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. PNAS (2019) 116:20969-20976.

Five selected postdoctoral studies (Advisor: Dr John Iafrate; Collaboration lab: Dr Keith Joung)

1. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature (2016) 529:490–495.
2. Tsai SQ*, Zheng Z*, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnology (2015) 33:187–198.
3. Huang J, Löhr JM, Nilsson M, Segersvärd R, Matsson H, Verbeke C, Heuchel R, Kere J, Iafrate AJ, Zheng Z (correspondence^#), Ye W^#. Mutation profiling of candidate genes in pancreatic ductal adenocarcinoma. Clinical Chemistry (2015) 61:1408-1416
4. Shaw A, Ou S, Bang Y, Camidge R, Solomon B, Salgia R, Riely G, Varella-Garcia M, Shapiro G, Costa D, Doebele R, Le LP, Zheng Z, Tan W, Stephenson P, Shreeve S, Tye L, Christensen J, Wilner K, Clark J, Iafrate AJ. Crizotinib in ROS1-Rearranged Non-Small Cell Lung Cancer. The New England Journal of Medicine (2014) 371:1963-1971.
5. Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J, Pao W, Engelman JA, Iafrate AJ, Le LP. Anchored multiplex PCR for targeted next-generation sequencing. Nature Medicine (2014) 20:1479-1484.

Five selected doctoral studies (Advisor: Dr Weimin Ye)

1. Zheng Z^#, Advani A, Melefors O, Glavas S, Nordstrom H, Ye W, Engstrand L, Andersson AF. Titration-free 454 sequencing using Y adapters. Nature Protocols (2011) 6:1367-1376.
2. Zheng Z^#, Advani A, Melefors O, Glavas S, Nordstrom H, Ye W, Engstrand L, Andersson AF. Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Research (2010) 38:e137.
3. Zheng Z, Jia Y, Hou L, Persson C, Yeager M, Lissowska J, Chanock S, Blaser M, Chow WH, Ye W. Genetic Variation in A4GNT in Relation to Helicobacter pylori Serology and Gastric Cancer Risk. Helicobacter (2009) 14:120–125.
4. Zheng Z, Margolis KL, Liu S, Tinker LF, Ye W, Women's Health Initiative I. Effects of estrogen with and without progestin and obesity on symptomatic gastroesophageal reflux. Gastroenterology (2008) 135:72-81.
5. Zheng Z, Nordenstedt H, Pedersen NL, Lagergren J, Ye W. Lifestyle factors and risk for symptomatic gastroesophageal reflux in monozygotic twins. Gastroenterology (2007) 132:87-95.

Position Available

We are looking for motivated individuals who are passionate about genomic medicine to join our lab as research assistants, PhD students and postdocs.

24 April 2024